@vitessce/all 4.0.7 → 4.0.9

package/dist-tsc/joint-file-types-legacy.d.ts

@@ -6,7 +6,7 @@ type legacyFileDefSchema = z.infer<typeof latestFileDefSchema> & {
 export declare function expandMoleculesJson(fileDef: legacyFileDefSchema): {
     fileType: string;
     coordinationValues: {
-        obsType: string;
+        obsType: any;
     };
     name?: string | undefined;
     url?: string | undefined;
@@ -27,9 +27,9 @@ export declare function expandMoleculesJson(fileDef: legacyFileDefSchema): {
 export declare function expandExpressionMatrixZarr(fileDef: legacyFileDefSchema): {
     fileType: string;
     coordinationValues: {
-        obsType: string;
-        featureType: string;
-        featureValueType: string;
+        obsType: any;
+        featureType: any;
+        featureValueType: any;
     };
     name?: string | undefined;
     url?: string | undefined;
@@ -63,7 +63,7 @@ export declare function expandRasterJson(fileDef: legacyFileDefSchema): {
         referrer?: string | undefined;
         integrity?: string | undefined;
     } | undefined;
-    coordinationValues?: Record<string, string> | undefined;
+    coordinationValues?: Record<string, any> | undefined;
     type?: string;
 }[];
 export declare function expandRasterOmeZarr(fileDef: legacyFileDefSchema): {
@@ -82,13 +82,13 @@ export declare function expandRasterOmeZarr(fileDef: legacyFileDefSchema): {
         referrer?: string | undefined;
         integrity?: string | undefined;
     } | undefined;
-    coordinationValues?: Record<string, string> | undefined;
+    coordinationValues?: Record<string, any> | undefined;
     type?: string;
 }[];
 export declare function expandCellSetsJson(fileDef: legacyFileDefSchema): {
     fileType: string;
     coordinationValues: {
-        obsType: string;
+        obsType: any;
     };
     name?: string | undefined;
     url?: string | undefined;
@@ -110,9 +110,9 @@ export declare function expandCellsJson(fileDef: legacyFileDefSchema): any[];
 export declare function expandClustersJson(fileDef: legacyFileDefSchema): {
     fileType: string;
     coordinationValues: {
-        obsType: string;
-        featureType: string;
-        featureValueType: string;
+        obsType: any;
+        featureType: any;
+        featureValueType: any;
     };
     name?: string | undefined;
     url?: string | undefined;
@@ -133,9 +133,9 @@ export declare function expandClustersJson(fileDef: legacyFileDefSchema): {
 export declare function expandGenesJson(fileDef: legacyFileDefSchema): {
     fileType: string;
     coordinationValues: {
-        obsType: string;
-        featureType: string;
-        featureValueType: string;
+        obsType: any;
+        featureType: any;
+        featureValueType: any;
     };
     name?: string | undefined;
     url?: string | undefined;
@@ -158,7 +158,7 @@ export declare function expandAnndataCellSetsZarr(fileDef: legacyFileDefSchema):
     fileType: string;
     options: any;
     coordinationValues: {
-        obsType: string;
+        obsType: any;
     };
     url: string | undefined;
     requestInit: {
@@ -181,7 +181,7 @@ export declare function expandAnndataExpressionMatrixZarr(fileDef: legacyFileDef
         initialFeatureFilterPath?: undefined;
     };
     coordinationValues: {
-        featureType: string;
+        featureType: any;
         obsType?: undefined;
         featureValueType?: undefined;
     };
@@ -205,9 +205,9 @@ export declare function expandAnndataExpressionMatrixZarr(fileDef: legacyFileDef
         initialFeatureFilterPath: any;
     };
     coordinationValues: {
-        obsType: string;
-        featureType: string;
-        featureValueType: string;
+        obsType: any;
+        featureType: any;
+        featureValueType: any;
     };
     url: string | undefined;
     requestInit: {

package/dist-tsc/joint-file-types-legacy.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"joint-file-types-legacy.d.ts","sourceRoot":"","sources":["../src/joint-file-types-legacy.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,CAAC,EAAE,MAAM,KAAK,CAAC;AAC7B,OAAO,KAAK,EAAE,mBAAmB,EAAE,MAAM,mBAAmB,CAAC;AAG7D,KAAK,mBAAmB,GAAG,CAAC,CAAC,KAAK,CAAC,OAAO,mBAAmB,CAAC,GAAG;IAC/D,IAAI,CAAC,EAAE,MAAM,CAAC;CACf,CAAC;AAEF,wBAAgB,mBAAmB,CAAC,OAAO,EAAE,mBAAmB;;;;;;;;;cAoRk23G,CAAC;eAAqC,CAAC;YAA+C,CAAC;YAAkC,CAAC;mBAAyC,CAAC;aAAmC,CAAC;gBAAsC,CAAC;gBAAsC,CAAC;iBAAuC,CAAC;;WAvRvt4G,MAAM;IAqBd;AAED,wBAAgB,0BAA0B,CAAC,OAAO,EAAE,mBAAmB;;;;;;;;;;;cAgQ213G,CAAC;eAAqC,CAAC;YAA+C,CAAC;YAAkC,CAAC;mBAAyC,CAAC;aAAmC,CAAC;gBAAsC,CAAC;gBAAsC,CAAC;iBAAuC,CAAC;;WAvRvt4G,MAAM;IAuCd;AAED,wBAAgB,gBAAgB,CAAC,OAAO,EAAE,mBAAmB;;;;;;cA8Oq23G,CAAC;eAAqC,CAAC;YAA+C,CAAC;YAAkC,CAAC;mBAAyC,CAAC;aAAmC,CAAC;gBAAsC,CAAC;gBAAsC,CAAC;iBAAuC,CAAC;;;WAvRvt4G,MAAM;IA0Dd;AAED,wBAAgB,mBAAmB,CAAC,OAAO,EAAE,mBAAmB;;;;;;cA2Nk23G,CAAC;eAAqC,CAAC;YAA+C,CAAC;YAAkC,CAAC;mBAAyC,CAAC;aAAmC,CAAC;gBAAsC,CAAC;gBAAsC,CAAC;iBAAuC,CAAC;;;WAvRvt4G,MAAM;IAqEd;AAED,wBAAgB,kBAAkB,CAAC,OAAO,EAAE,mBAAmB;;;;;;;;;cAgNm23G,CAAC;eAAqC,CAAC;YAA+C,CAAC;YAAkC,CAAC;mBAAyC,CAAC;aAAmC,CAAC;gBAAsC,CAAC;gBAAsC,CAAC;iBAAuC,CAAC;;WAvRvt4G,MAAM;IAmFd;AAED,wBAAgB,eAAe,CAAC,OAAO,EAAE,mBAAmB,SA0C3D;AAED,wBAAgB,kBAAkB,CAAC,OAAO,EAAE,mBAAmB;;;;;;;;;;;cAsJm23G,CAAC;eAAqC,CAAC;YAA+C,CAAC;YAAkC,CAAC;mBAAyC,CAAC;aAAmC,CAAC;gBAAsC,CAAC;gBAAsC,CAAC;iBAAuC,CAAC;;WAvRvt4G,MAAM;IAiJd;AAED,wBAAgB,eAAe,CAAC,OAAO,EAAE,mBAAmB;;;;;;;;;;;cAoIs23G,CAAC;eAAqC,CAAC;YAA+C,CAAC;YAAkC,CAAC;mBAAyC,CAAC;aAAmC,CAAC;gBAAsC,CAAC;gBAAsC,CAAC;iBAAuC,CAAC;;WAvRvt4G,MAAM;IAmKd;AAeD,wBAAgB,sBAAsB,CAAC,OAAO,EAAE,mBAAmB,SAkDlE;AAED,wBAAgB,yBAAyB,CAAC,OAAO,EAAE,mBAAmB;;;;;;;;;;;;;;;;;;IAiBrE;AAED,wBAAgB,iCAAiC,CAAC,OAAO,EAAE,mBAAmB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;KA6B7E"}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@vitessce/all",
-  "version": "4.0.7",
+  "version": "4.0.9",
   "author": "HIDIVE Lab at HMS",
   "homepage": "http://vitessce.io",
   "repository": {
@@ -17,38 +17,39 @@
   ],
   "dependencies": {
     "zod": "^3.21.4",
-    "@vitessce/constants-internal": "4.0.7",
-    "@vitessce/styles": "4.0.7",
-    "@vitessce/csv": "4.0.7",
-    "@vitessce/description": "4.0.7",
-    "@vitessce/error": "4.0.7",
-    "@vitessce/feature-list": "4.0.7",
-    "@vitessce/heatmap": "4.0.7",
-    "@vitessce/abstract": "4.0.7",
-    "@vitessce/glb": "4.0.7",
-    "@vitessce/json": "4.0.7",
-    "@vitessce/genomic-profiles": "4.0.7",
-    "@vitessce/layer-controller": "4.0.7",
-    "@vitessce/layer-controller-beta": "4.0.7",
-    "@vitessce/obs-sets-manager": "4.0.7",
-    "@vitessce/link-controller": "4.0.7",
-    "@vitessce/ome-tiff": "4.0.7",
-    "@vitessce/plugins": "4.0.7",
-    "@vitessce/scatterplot-gating": "4.0.7",
-    "@vitessce/schemas": "4.0.7",
-    "@vitessce/spatial": "4.0.7",
-    "@vitessce/scatterplot-embedding": "4.0.7",
-    "@vitessce/spatial-beta": "4.0.7",
-    "@vitessce/statistical-plots": "4.0.7",
-    "@vitessce/status": "4.0.7",
-    "@vitessce/vit-s": "4.0.7",
-    "@vitessce/globals": "4.0.7",
-    "@vitessce/spatial-zarr": "4.0.7",
-    "@vitessce/zarr": "4.0.7",
-    "@vitessce/spatial-accelerated": "4.0.7",
-    "@vitessce/biomarker-select": "4.0.7",
-    "@vitessce/spatial-three": "4.0.7",
-    "@vitessce/neuroglancer": "4.0.7"
+    "@vitessce/constants-internal": "4.0.9",
+    "@vitessce/styles": "4.0.9",
+    "@vitessce/error": "4.0.9",
+    "@vitessce/csv": "4.0.9",
+    "@vitessce/description": "4.0.9",
+    "@vitessce/abstract": "4.0.9",
+    "@vitessce/annotation-controller": "4.0.9",
+    "@vitessce/feature-list": "4.0.9",
+    "@vitessce/genomic-profiles": "4.0.9",
+    "@vitessce/json": "4.0.9",
+    "@vitessce/glb": "4.0.9",
+    "@vitessce/heatmap": "4.0.9",
+    "@vitessce/layer-controller-beta": "4.0.9",
+    "@vitessce/link-controller": "4.0.9",
+    "@vitessce/layer-controller": "4.0.9",
+    "@vitessce/scatterplot-embedding": "4.0.9",
+    "@vitessce/scatterplot-gating": "4.0.9",
+    "@vitessce/ome-tiff": "4.0.9",
+    "@vitessce/spatial-beta": "4.0.9",
+    "@vitessce/plugins": "4.0.9",
+    "@vitessce/obs-sets-manager": "4.0.9",
+    "@vitessce/spatial": "4.0.9",
+    "@vitessce/statistical-plots": "4.0.9",
+    "@vitessce/schemas": "4.0.9",
+    "@vitessce/zarr": "4.0.9",
+    "@vitessce/spatial-zarr": "4.0.9",
+    "@vitessce/globals": "4.0.9",
+    "@vitessce/spatial-three": "4.0.9",
+    "@vitessce/spatial-accelerated": "4.0.9",
+    "@vitessce/status": "4.0.9",
+    "@vitessce/biomarker-select": "4.0.9",
+    "@vitessce/neuroglancer": "4.0.9",
+    "@vitessce/vit-s": "4.0.9"
   },
   "devDependencies": {
     "@types/react": "^19.0.0",

package/src/base-plugins.ts

@@ -76,6 +76,8 @@ import {
   meshGlbSchema,
   ngPrecomputedMeshSchema,
   ngPointAnnotationSchema,
+  annotationStoryObj,
+  annotationShapesArray,
 } from '@vitessce/schemas';
 
 // Register view type plugins
@@ -93,6 +95,7 @@ import { FeatureListSubscriber } from '@vitessce/feature-list';
 import { LayerControllerSubscriber } from '@vitessce/layer-controller';
 import { LayerControllerBetaSubscriber } from '@vitessce/layer-controller-beta';
 import { LinkControllerSubscriber } from '@vitessce/link-controller';
+import { AnnotationControllerSubscriber } from '@vitessce/annotation-controller';
 import { StatusSubscriber } from '@vitessce/status';
 import { HiGlassSubscriber, GenomicProfilesSubscriber } from '@vitessce/genomic-profiles';
 import { NeuroglancerSubscriber } from '@vitessce/neuroglancer';
@@ -107,6 +110,7 @@ import {
   FeatureStatsTableSubscriber,
   CellSetCompositionBarPlotSubscriber,
   FeatureSetEnrichmentBarPlotSubscriber,
+  SingleCellSetSelectorSubscriber,
 } from '@vitessce/statistical-plots';
 
 // Register file type plugins
@@ -130,6 +134,7 @@ import {
   JsonLoader,
   ObsSegmentationsJsonLoader,
   ObsSetsJsonLoader,
+  AnnotationStoryJsonLoader,
   // Legacy
   RasterJsonAsImageLoader,
   RasterJsonAsObsSegmentationsLoader,
@@ -280,6 +285,7 @@ export const baseViewTypes = [
   makeViewType(ViewType.DOT_PLOT, DotPlotSubscriber),
   makeViewType(ViewType.VOLCANO_PLOT, VolcanoPlotSubscriber),
   makeViewType(ViewType.FEATURE_STATS_TABLE, FeatureStatsTableSubscriber),
+  makeViewType(ViewType.SINGLE_OBS_SET_SELECTOR, SingleCellSetSelectorSubscriber),
   makeViewType(ViewType.BIOMARKER_SELECT, BiomarkerSelectSubscriber),
   makeViewType(ViewType.BIOMARKER_SELECT_ALT, BiomarkerSelectAltSubscriber),
   makeViewType(ViewType.LINK_CONTROLLER, LinkControllerSubscriber),
@@ -289,6 +295,7 @@ export const baseViewTypes = [
   makeViewType(ViewType.SAMPLE_SET_PAIR_MANAGER, SampleSetPairManagerSubscriber),
   makeViewType(ViewType.OBS_SET_COMPOSITION_BAR_PLOT, CellSetCompositionBarPlotSubscriber),
   makeViewType(ViewType.FEATURE_SET_ENRICHMENT_BAR_PLOT, FeatureSetEnrichmentBarPlotSubscriber),
+  makeViewType(ViewType.ANNOTATION_CONTROLLER, AnnotationControllerSubscriber),
 ];
 
 export const baseFileTypes = [
@@ -306,6 +313,7 @@ export const baseFileTypes = [
   // All JSON file types
   makeFileType(FileType.OBS_SEGMENTATIONS_JSON, DataType.OBS_SEGMENTATIONS, ObsSegmentationsJsonLoader, JsonSource, z.null()),
   makeFileType(FileType.OBS_SETS_JSON, DataType.OBS_SETS, ObsSetsJsonLoader, JsonSource, z.null()),
+  makeFileType(FileType.ANNOTATION_STORY_JSON, DataType.ANNOTATION_STORY, AnnotationStoryJsonLoader, JsonSource, z.null()),
   // All AnnData file types
   ...makeZarrFileTypes(FileType.OBS_SETS_ANNDATA_ZARR, DataType.OBS_SETS, ObsSetsAnndataLoader, AnnDataSource, obsSetsAnndataSchema),
   ...makeZarrFileTypes(FileType.OBS_EMBEDDING_ANNDATA_ZARR, DataType.OBS_EMBEDDING, ObsEmbeddingAnndataLoader, AnnDataSource, obsEmbeddingAnndataSchema),
@@ -654,6 +662,14 @@ export const baseCoordinationTypes = [
   new PluginCoordinationType(CoordinationType.FEATURE_LABEL_SIGNIFICANCE_THRESHOLD, 0.01, z.number().nullable()),
   new PluginCoordinationType(CoordinationType.FEATURE_POINT_FOLD_CHANGE_THRESHOLD, 1.0, z.number().nullable()),
   new PluginCoordinationType(CoordinationType.FEATURE_LABEL_FOLD_CHANGE_THRESHOLD, 5.0, z.number().nullable()),
+  // Annotation frames
+  new PluginCoordinationType(CoordinationType.ANNOTATION_STORY, null, annotationStoryObj.nullable()),
+  new PluginCoordinationType(CoordinationType.ANNOTATION_SHAPES, null, annotationShapesArray.nullable()),
+  new PluginCoordinationType(CoordinationType.ANNOTATION_FRAME_INDEX, null, z.number().nullable()),
+  new PluginCoordinationType(CoordinationType.ANNOTATION_OVERLAY_VISIBLE, true, z.boolean()),
+  new PluginCoordinationType(CoordinationType.ANNOTATION_TRANSITION_DURATION, 0, z.number()), // TODO: make this non-zero by default?
+  new PluginCoordinationType(CoordinationType.ANNOTATION_SEMANTIC_ZOOM, true, z.boolean()),
+  new PluginCoordinationType(CoordinationType.ANNOTATION_EDITABLE, false, z.boolean()),
 ];
 
 export const baseAsyncFunctions = [

package/src/index.ts

@@ -7,6 +7,13 @@ export {
   PluginAsyncFunction,
 } from '@vitessce/plugins';
 export { z } from '@vitessce/schemas';
+export {
+  hasAnnotationControllerView,
+  addAnnotationControllerView,
+  isAnyAnnotationEditing,
+  enableAnnotationEditing,
+  disableAnnotationEditing,
+} from '@vitessce/annotation-controller';
 export {
   useCoordination,
   useGridItemSize,